Using multiple alignments to improve seeded local alignment algorithms | Zendy

Jason Flannick | Zendy

AI Assistant Blog Pricing

Home ZAIA Blog

Open Access

Using multiple alignments to improve seeded local alignment algorithms

Author(s) -

Jason Flannick

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki767

Subject(s) - search engine indexing , alignment free sequence analysis , sequence alignment , multiple sequence alignment , biology , homology (biology) , smith–waterman algorithm , genome , algorithm , structural alignment , computer science , data mining , computational biology , information retrieval , genetics , peptide sequence , gene

Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising regions of the multiple alignment. We have implemented Typhon, a local alignment tool that incorporates our indexing algorithm, which our test results show to be more sensitive than algorithms that index only a sequence. This suggests that when applied on a whole-genome scale, Typhon should provide improved homology searches in time comparable to existing algorithms.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.

Having issues? You can contact us here

Accelerating Research